Wednesday, September 16, 2015

Philosophy and reality

The figure on the right has been circulating on Facebook. It suggests that philosophers in the Philosophy of Science are perplexed about the nature of reality. Some might actually believe that reality doesn't exist.

The diagram evokes the memory of undergraduate debates about whether that chair actually exists or whether we live in the matrix. These debates seem silly on the surface but they are actually very important in classes devoted to logic and critical thinking. They provide real experience in thinking.

However, there are issues in philosophy that seem silly to an outsider. For example, many philosophers are theologians and they still argue for the existence of gods. The ontological argument is still taken seriously by many philosophers. It seems to me that the question "Do gods exist?" should have been settled a long time ago in philosophy departments. There doesn't seem to be any legitimate arguments in favor of gods but many philosophers are still debating that very point.

There are also debates about ethics—that's Cris DiCarlo's current area of expertise. The idea that there are immutable, universal, moral absolutes is still a hot topic in philosophy and that seems very strange for a discipline that prides itself on logic and rationality. Other big questions of philosophy are "free will vs. determinism," and the mind-body problem. Many scientists think these issues have been resolved in favor of determinism and the rejection of dualism but philosophers are still making up their minds.

Lots of universities have departments called "History and Philosophy of Science." Professors in those departments are often interested in the history of scientific ideas and their work is very interesting. Others are interested in epistemology—also an interesting and complicated subject that's worth exploring. I recently read a book on the Demarcation Problem and I found it fascinating. I'm a great admirer of Maarten Boudry [Science Doesn't Have All the Answers but Does It Have All the Questions?].

There are issues in the philosophy of science where philosophers seem to have gone off the rails and that's why some scientists have been critical of philosophy. Philosophers who criticize scientists for the sin of scientism and who promote the idea of methodological naturalism do not seem to be exercising the most fundamental rules of logic and rationalism yet they are considered to be good philosphers: Massimo Pigliucci, for example [What Kind of Knowledge Does Philosophy Discover?].

Some well-respected philosophers have promoted really silly ideas that should have been soundly rejected by all intelligent philosophers. It's astonishing that a famous philosopher of science could be be respected for arguing that omnipotent god(s) could direct the course of evolution by creating mutations that we cannot detect above background [e.g. The Problem with Philosophy: Elliott Sober]. I'm not disputing the truth of such an argument but surely it's been around for a long time and doesn't deserve to be taken seriously?

This brings us back to the discussion about reality. John Wilkins has a short video on Scientific Realism & Structural Realism where he discusses the issue.

Here's the description posted by producer Adam Ford ....

Scientific realism is, at the most general level, the view that the world described by science is the real world, as it is, independent of what we might take it to be. Within philosophy of science, it is often framed as an answer to the question "how is the success of science to be explained?" The debate over what the success of science involves centers primarily on the status of unobservable entities apparently talked about by scientific theories. Generally, those who are scientific realists assert that one can make valid claims about unobservables (viz., that they have the same ontological status) as observables, as opposed to instrumentalism.
Points Covered:
IS THERE SUCH A THING AS A GENE?
ARE SPECIES REAL?
WHAT DOES SCIENCE IMPLY?
WHAT DOES SCIENCE MEAN?
QUESTIONS OF REALITY
ANTI-REALISM
IS PHILOSOPHY A WASTE OF TIME?

This gets complicated. First you have to understand what John means by "science." He means the work produced by scientists (geologists, biologists, physicists, chemists, astronomers etc.). I don't agree with that definition but let's go with it for now.1

I think that 99.9% of what scientists discover is real and that science has revealed the real world. I think that DNA is real, RNA polymerase is real, enzymes are real and some cells really do convert glucose to CO2 and use the energy released to create a proton gradient. I think that genomes are real and so are transposons. I think that evolution is real—it actually occurs.

I'm not sure whether John Wilkins agrees with me that science is, for the most part, describing the real world.

John points out in the video that there was some question in the past whether electrons, protons, and neutrons were real or not. Presumably, he agrees that the issue has now been settled in favor of reality. What that means is that in the past there may have been some philosophers who didn't know whether electrons were real or just conceptual devices. That doesn't mean they were justified in declaring that science does not describe the real world, does it? The best they could have said, logically, is that they don't know whether electrons are real or not.

I define a gene as "a DNA sequence that is transcribed to produce a functional product" [What Is a Gene?]. That's a good working definition, IMHO, but it's not perfect. Very few definitions are perfect in biology because it's a very messy science. Evolution does that.

There are exceptions to the definition (e.g. RNA genes) and there are ambiguous examples (e.g. operons) but that doesn't mean that the gene isn't real. Workers in the history and philosophy of science have done a good job of highlighting the problems with defining a gene. For example, John's colleague Paul Griffiths has published some excellent papers on the problem.

Now, it's true that "gene" is sometimes used to represent a concept rather than a real entity the way molecular biologists and biochemists think about it. In that sense the word "gene" can be taken as "unreal" but isn't that just another way of saying "ill-defined" or "metaphor"?

I don't see why this is such an important issue in the philosophy of science. Is that really a "hot-button issue" as John describes it? He asks, "Are the things that science tells us exist in the world, real?"

John, the answer is "yes," with only minor exceptions.

There are some things in biology that count as "conceptual concepts" and, in that sense, they are not "real." I'm thinking of "junk DNA" as an example. The term is used as a short-hand for stretches of DNA that have no biological function and could be removed from the organism without harm. In evolutionary biology we talk about "selection coefficients" as a way of describing the the tendency of a trait to increase in frequency in a population due to natural selection. Selection coefficients are not real, three-dimensional, entities but everybody knows that. Surely it's not a hot-button issue?

John is an expert on the meaning of the word "species" and he has made some important contributions to the scientific literature by reviewing the history of the term and its current meaning. Like the word "gene," the word "species" describes something that cannot be rigorously defined. That's because species are fluid entities that are constantly being formed and dissipated and because there are no unique attributes that distinguish all species from all other species. That's the nature of biology. It doesn't mean that Homo sapiens is not "real" in a meaningful practical sense even though we may never know for sure whether Neanderthals were the same species or a different species.

In biology we do the best we can with terms like "species" and "gene" but to question whether they represent "real" things or not seems, well, ... unreal.

I think I can speak for most scientists when I say that our theories and models are intended to describe the real world as it actually exists. John seems to agree since he is sympathetic to the idea of "structural realism." Good for him but what about those other philosophers who are anti-realists? Is that really a respectable position in the philosophy of science or is it just that philosophers like to quibble?

John says, "Philosophers tend to ask questions that scientists either don't think are terribly interesting or don't think can be answered and, as a result, a lot of scientists think that philosophy is actually a waste of time." That's only partially true. In addition, many of us think that philosophers are still interested in questions that CAN be answered but they just don't like the answer.

I don't think it's terribly interesting to debate whether gods could make undetectable mutations and it's hard to respect philosophers who think this is still worth discussing. I don't think there can be a definitive answer to questions such as "what is a gene" and "what is a species" so it's time to move on. The fact that we can't answer those specific questions in biology does not mean that there's a reality crisis.

I think that prokaryotic protein-coding bits of DNA are transcribed by RNA polymerase to produce a real RNA molecule that can be translated by real ribosomes to make real proteins inside real cells. Philosophers who question whether this view of the world is real or not are not going to get a lot of respect from biochemists and molecular biologists.

I think that those philosophers who say that science is restricted to methodological naturalism are dead wrong. I can't believe that this is still a hot topic in philosophy.

I have never said that philosophy is a waste of time but I have said that some aspects of philosophy are questionable. Many philosophers are too tolerant of silly ideas that permeate their field. All disciplines have kooks but most of them don't let the kooks run the asylum.

John once told me that he's a philosophical pragmatist. I think that's a reasonable position to take.

1. One of the problems with many philosophers is that they make assumptions about definitions without explaining that it's just their opinion. There are other definitions of "science" that are popular among philosophers, and scientists. Those other meanings change the argument that John is making. The nature of science is a more important topic in the philosophy of science than the nature of reality. Are theories and models of philosophy fundamentally different from theories and models of biology, chemistry, and physics? What about theories and models in history, English literature, and religion? Are they real? Do philosophers question those theories?

117 comments
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I would like to introduce the word "realish". Species are sorta-kinda real, i.e. they're realish. That is, the term "species" is a useful abstraction that describes some aspects of the non-uniform distribution of the diversity and disparity of life. It works better in some cases than others.

Genes are realish too. But I don't see the difficulty with RNA genes that you suggest. Surely they are indeed transcribed and make a functional product. I do however see some other problems, as what we call genes often have both 5' and 3' untranscribed regions, and those are considered parts of the genes. Perhaps a gene needs a transcribed bit, but it can contain other bits too. Is a promoter region part of its gene, or is it a non-gene that affects a nearby gene?

I am accustomed to seeing the definition of 'gene' that Larry had given, although I prefer a slightly more extended definition: 'A gene is a region of DNA that is needed to code for a functioning molecule of RNA'. To me this not only includes the coding region, but also the regulatory regions like the promoter and other regions that function as enhancers and silencers. I am inclined to like this definition since we often describe mutations of regulatory regions as mutations of a gene, so now our terminology seems more consistent.Like any definition of a gene this one also has problems since it is difficult to identify all regulatory regions.

My own take on species is close to John's. A "species" is a model we have in our minds, of a group of individuals that are genetically isolated from other such groups but who can contribute to a common gene pool. As a model, in many cases it does not exactly correspond to reality. So species are not exactly real. But nevertheless the model is useful for predicting outcomes. It's "realish".

The same holds for entities like "population". And sometimes even for "individual".

Having such a Model Species Definition is unpopular with many evolutionary biologists, who want a criterion that can be used to make yes/no decisions in real cases.

However, I find the idea of God-guided evolution by intervention in mutations both logically and theologically unacceptable.

If God really guided the evolution, that would contradict His own statement in the Bible about the act of creation. If God just created a simple life form and let it evolve into all the known life forms, why not state it clearly in the Bible instead of the describing the creation of life forms according to their kinds? Gen 1:20-27

If God intervenes in the mutations, even if in only some of them, to guide the evolution process, that would make Him, at least to some degree, responsible for the side effects of at least some of those mutations causing diseases, like cancer, abnormalities and death.

This idea also contradicts the Bible teaching, which clearly states that God is not responsible for evil things happening to humans, such as diseases and death due to them.

The Bible clearly states that after the rebellion in the Garden of Eden, Adam and Eve separated themselves from the source of life-God and brought upon themselves and their offspring all the imperfections, such as diseases and death.

Since God allowed some time to pass to resolve the issues raised due to the rebellion, he doesn’t interfere in the progress of those issues as that would mean that He would be cooperating with Satan and his followers and interfering with the progress and the resolution of those issues. It would simply be unjust and one of God’s dominating qualities is justice.

Job 2:7

“ 7 So Satan went out from the presence of Jehovah and struck Job with painful boils from the sole of his foot to the crown of his head”

Well, those who believe in guided evolution already figured out the bible is not the ultimate source of truth that some pretend it is, but they're still not ready to get rid of the idea that a "god" is needed to explain stuff. Or what's otherwise known as "grasping at straws"

If the Bible is not the ultimate source of truth, and the shepherds had no microscopes or education of todays scientists, how did they find out this truth few thousand years ago that scientists discovered just in the last century?

Ps 139:16

"16 Your eyes even saw me as an embryo;

All its parts were written in your book

Regarding the days when they were formed,

Before any of them existed."

How did they know about information written down that was required for embryo's part to develop?

"How did they know about information written down that was required for embryo's part to develop?"

Basically because your version of the psalm is a completely different version from the one main stream bibles use. So, the more likely explanation is the bit about embryo's got added in to give your version of the bible some scientific cachet, a long time after scientists started using microscopes. Van Leeuwenhok did some marvelous work with a microscope in the 17th century already, certainly not last century.

Newbie IIRC is a Jehovah's Witness, or sounds like one, so they're totes logical.

How did they know about information written down that was required for embryo's part to develop?

There isn't any information "written down" in any "book" causing an embryo to develop. There is sequential information in a charged acidic double-helical biopolymer which is never mentioned in your Bible.

The Bible passage you quote, though it is a modern translation influenced by modern scientific knowledge, does not assert there was any information in DNA (which is what you're implying) or a "book" or wherever, guiding the embryonic development process.

Your Bible passage alleges that there's a book with a list of body parts. There is no such book, and the DNA that guides embryonic development is not a list of body parts. If in fact it is a prediction of Christianity that ''the Bible will accurately describe the mechanism of embryonic development", then the failure of this prediction falsifies Christianity. ... If that's not a prediction of Christianity, why are you trying to pass it off as such?

You know, the Bible is practically the only document of Classical Hebrew, so if a word occurs only once and twice in the Bible, in a context that doesn't clarify its meaning, all readings are speculative. The word golem in Ps 139:16 can be loosely translated as "shapeless mass" (like a lump of clay before Yahweh kneads it into a human shape). It's clearly derived from the verb galam 'to wrap up, roll together', which doesn't help to reconstruct its precise meaning.

But we can be more imaginative, maybe even more than the JW editors of the "New World Translation". Who can prove that golem doesn't mean 'zygote', and that the passage shouldn't be read as follows:

Your eyes even saw my zygote under a microscope; the correct sequence in which my body parts were to develop was intelligently pre-programmed in the DNA sequence before they came into existence.

-- eh? Of course Hebrew-speakers had no concepts like 'microscope' or 'genome', hence the circumlocutions.

But still I think the "lump of clay" imagery is closer to what the Biblical authors really intended. Newbie didn't quote the immediately preceding verse. Here is the AV translation (I don't care for this New World nonsense, though it doesn't say anything radically different in this case):

My substance was not hid from thee, when I was made in secret, and curiously wrought in the lowest parts of the earth.

How could the folks who composed the Psalms know that children were made in the depths of the earth?

There is more:How did the shepherds know that "God is stretching out out the heavens? Or in modern terms that the universe is actually expanding?

In 1999 I believe it was proven that the heavens are expanding, only 3000 years after the simple bible shepherded wrote this. This fact will obviously be ignored by the ones who made up their mind before the evidence crept in.

Yea, how did those shepherds know that the earth is flat and circular.

It's a miracle, praise god.

Hey Newbie, did you know that the Koran predicted embryology as well and continental drift to boot, which your book seems to have missed out on.

As the Norse used to say "My God Has A Hammer, Your God Was Nailed To A Cross". Yours is but a young and upstart religion. Come back in a few thousand years and then perhaps we can start to take your seriously.

How did those shepherds know that Earth was circular, not spherical, and the sky was like the roof of a tent stretched out above us? Only explanation: an infallible omniscient being told them. About the circular Earth. And the tent sky.

Hey Newbie, don't you JWs believe that the world will end within the lifetime of those who were baptized and witnessed the world-shattering events of 1914? How many of those baptized witnesses are left alive after 101 years?

For those who think that the freak show being put on by Newbie is but a mild eccentricity of a charming but damaged victim of religious indoctrination, this is the same Newbie who defends the murder of children by denying them life saving blood transfusions.

Using the same malodorous book.

Beliefs have consequences, some have little immediate impact, other than providing a few moments of low quality entertainment at the expense of a delusional idiot, others have a devastating effect on the lives of innocent children.

It is informative to see these beliefs espoused by the same person and perhaps it may cause one to form a different opinion of the next person that promulgates seeming harmless fairy tales using revelation, dogma and authority as the sole components of their intellectual tool kit.

For children to be denied blood transfusion, they would have to be born first. Unfortunately, due to many millions of abortions happening every year the only children having the possibility of the denial of blood transfusion are the children of the people who give them the chance to live first. Which denial do you find more disturbing?

Your knowledge is very limited when it comes to the scriptures. The Hebrew language and it's translation to the Greek scriptures help to understand the real meaning of the words. Piotr's bringing in the "golem" tells me he is at the same level. I don't think he understands the issue at all and neither do you.

But of course, Newbie, you thoroughly understand "the scriptures", eh? Anyone who isn't Newbie, or at least a jehova's witness, doesn't understand "the scriptures", right? Hmm, every thumper I've ever come across believes that they understand "the scriptures" and that their particular version/interpretation is the one that is true. There sure are a lot of disagreements between thumpers when it comes to "the scriptures", even though "the scriptures" are alleged to be 'God's word'.

How many people have been and still are oppressed, deprived, harassed, coerced, abused, enslaved, imprisoned, tortured, robbed, raped, murdered, conquered, etc., because of different versions/interpretations and self-righteous enforcement of "the scriptures"? The allegedly omnipotent, omniscient, omnipresent, omnibenevolent, supernatural, perfect, christian 'God' thing obviously isn't a good communicator of its word. Maybe the 'God' thing should get some lessons in good communication from Will Rogers, Mark Twain, or Dr. Seuss.

The 'God(s)' in religions other than christianity are obviously not good communicators of their 'word' either. The so-called 'Gods' that people believe in, worship, and promote sure are a bunch of impotent screwups.

By the way, Newbie, being a mindless puppet for "the scriptures" is a waste of your life.

Unfortunately, due to many millions of abortions happening every year the only children having the possibility of the denial of blood transfusion are the children of the people who give them the chance to live first.

Not to mention the millions more spontaneously aborted by God before they have the chance to live.

The Hebrew language and it's translation to the Greek scriptures help to understand the real meaning of the words. Piotr's bringing in the "golem" tells me he is at the same level.

Translation into Greek helps you to understand a Hebrew hapax legomenon? I didn't "bring in the golem"; the authors of the Bible did. Golem is the word used in the Bible -- the one your JW authorities arbitrarily interpret as 'embryo'. Anyway, "knowledge of the scriptures" is completely irrelevant to our understanding of the real world.

It doesn't mean that Homo sapiens is not "real" in a meaningful practical sense even though we may never know for sure whether Neanderthals were the same species or a different species.

Is there interesting science on this topic? We've got some Neanderthal genes and could therefore interbreed with Neanderthals and produce fertile offspring, so I suppose that's one strike against the idea of separate species. But apparently neanderthelensis is classified as a different species than sapiens - why is that?

Because Neanderthals were defined prior to molecular evidence on the basis of fossils. And it's not like there aren't modern cases of interbreeding species even today -- Wolves are Canis lupis and coyotes Canis latrans and yet "coywolfs" (their mutual offspring) exist in nature.

As I understand it, this question as to whether Neanderthals are a separate species from Sapiens is an ongoing controversy. Some consider that they are sub-species of Homo sapiens, e.g. humans are Homo sapiens sapiens and Neanderthals are Homo sapiens neanderthalensis.

I could be wrong here, but my understanding is that the A blood group isotope would but A-type humans and chimps in the same species whereas the B blood group isotype humans and chimps would be in a separate species. Basically I don't think having 'neandestal genes' tells us much about species demarcations.

40+ species of duck can interbreed and many of the hybrids are fully fertile. With duck, hybrids are possible even between different genera (e.g. mallards x Muscovy ducks, those this particular hybrid, called the mulard, is sterile).

@judmarc Not sure how the BSC relates to my comment regarding gene descent. The idea that sapiens have neandertal genes, doesn't necessarily mean the two groups actively interbred but instead be an outcome of common ancestry. At least that was what I was getting at. The BSC is of quite limited value when you consider all of life, but it is useful when thinking about humans, which I guess is why it is a default position.

I don't know about coywolves, but coydogs are fertile. However, they come into breeding condition earlier than coyotes do (so they can breed only with dogs, which don't have such restricted fertile seasons as wolves) and the puppies are born in winter, which means that in the wild they are unlikely to survive in highly seasonal climate, though they could in some areas.

The question of how to classify Homo sapiens vs neandertals is one of the classic problems for taxonomy. Neandertals and modern humans were isolated for a long time and were physically different. Calling them different species therefore seems reasonable. When they met after the long isolation, they could and did interbreed to produce fertile offspring -- at least once, maybe more, maybe often. We don't know. If they interbred often when they met, maybe they should be considered members of the same species (probably different subspecies). If interbreeding was rare or most offspring were sterile, calling them different species would be reasonable.

This is one of the taxonomic cases where the labels (species vs. subspecies vs. just races) don't matter. We need to know what they were like and their relationships are, but we see that the situation is complex. In a case like this, we need labels, but the choice of label is arbitrary. It's not worth fighting over, though I know some people will.

Thanks bwilson. I don't know what a Neanderthal contribution of up to 4% of the genome in some modern human populations says, if anything, about frequency of interbreeding to produce fertile offspring.

If "coydogs" survive in their usual (domestic) environment, I don't think there is a problem re their making a problem for the species definition.

So dogs tie wolves and coyotes together? (Through a series of breeds.) I didn't see that one coming!

@judmarc: As the recent PBS series about human origins told us, apparently you can scramble together 1/3 of a Neanderthal from the on average 1-3 % scraps we have per individual. I am not sure what that tells us either...

If coydogs survive and reproduce, they reproduce only with dogs, and their genes mix into the large and varied dog gene pool.

Coywolves also exist. In most areas they are rare. However, the "coyotes" invading the northeastern US (and presumably Canada) have clear coywolf ancestry. Though I think they have more coyote than wolf genes -- would have to look that up to be sure.

John points out in the video that there was some question in the past whether electrons, protons, and neutrons were real or not. Presumably, he agrees that the issue has now been settled in favor of reality.

A better example is the quantum vacuum. Whether it exists as a physical entity is the subject of debate. However, it's existence is assumed in order to compute the anomalous magnetic moment of the electron, which seems to be due to the interaction of the electron with the quantum vacuum (e.g. the vacuum corrections of quantum-electrodynamics).

Quantum vacuum must be real to compute the Kasimir force, which is measurable.

To compute the anomalous magnetic moment, you just need a huge number of Feynman diagrams which represent interactions between virtual particles that can't be detected, e.g. a photon splits into an electron-positron pair ("loop") that recombine to form a new photon, etc.

To compute the AMM, you only need some kinds of virtual particles and their interactions. To compute the Kasimir Force, technically you need to know all kinds of virtual particles and their interactions. This is more relevant to the quantum vacuum as a whole.

Some of these questions, like "Are species real?" seem to me not ontological problems ("How do we define reality?") but instead just the Sorites paradox: "At what point does 'stubble' become a 'beard'"? This is a problem with "gray areas" messing up simple, absolute definitions independent of context.

The Sorites paradox should be separated from ontological questions such as, "Are virtual particles real? Are alternate quantum timelines, in the 'Many Worlds Interpretation', real?" I'd say "yes" and "yes", and watch the conservatives' heads explode.

Virtual particles is a misnomer, they exist but are best seen as collective phenomena:

"The best way to approach this concept, I believe, is to forget you ever saw the word “particle” in the term. A virtual particle is not a particle at all. It refers precisely to a disturbance in a field that is not a particle. A particle is a nice, regular ripple in a field, one that can travel smoothly and effortlessly through space, like a clear tone of a bell moving through the air. A “virtual particle”, generally, is a disturbance in a field that will never be found on its own, but instead is something that is caused by the presence of other particles, often of other fields."

"Exactly the same equations that tell us about photons also tell us about how these disturbances work; in fact, the equations of quantum fields guarantee that if nature can have photons, it can have these disturbances too. Perhaps unfortunately, this type of disturbance, whose details can vary widely, was given the name “virtual particle” for historical reasons, which makes it sound both more mysterious, and more particle-like, than is necessary. [Students of math and physics will recognize real photons as solutions of a wave equation, and virtual photons as related to the Green function associated with this equation.]"

"So we learn that particles are just not simple objects, and although I often naively describe them as simple ripples in a single field, that’s not exactly true. Only in a world with no forces — with no interactions among particles at all — are particles merely ripples in a single field! Sometimes these complications don’t matter, and we can ignore them. But sometimes these complications are central, so we always have to remember they are there."

I think the statement that "many of us think that philosophers are still interested in questions that CAN be answered but they just don't like the answer" clarifies a problem that occurs in the interaction between scientists and philosophy.

While, it might be true that this is what many scientists *think* many philosophers do, I doubt that what those scientists think is true. I do not see that many philosophers throw unreasonable doubts on answers they should reasonably accept and that they do so either merely "because they like to quibble" or solely because the obvious answer doesn't fit their worldview.

John Wilkins certainly has a point when he says that scientists who see philosophy as a waste of time might do so simply because they don't understand what philosophy is up to.

Scientific realism is a case in point. It isn't my favorite subject, but I am pretty sure that, contrary to what Larry suggests, anti-realists nowadays do *not* claim that reality doesn't exist. What they do claim is that we should not pretend that the structures science posits to explain or predict our observations are meant to describe an underlying reality. I know that this sounds bizarre to most biologists (it sounds bizarre to me too), but I know several theoretical physicists who find the idea that their theories do or should describe an underlying reality equally bizarre. The view that belief and desire models do not describe a reality underlying our behavior and are not intended to do so is, as far as I know, pretty standard in cognitive science. So there really are scientists who don't strive for theories and models that describe an underlying reality and who don't think that striving for such theories is a hallmark of good science.

Now, as scientists differ in opinions about this issue, why is it questionable when philosophers try to work out the different positions and discuss their pro- and contra's when the scientists themselves don't do so (perhaps because the answer is obvious from their point of view, perhaps because they lack the time or the focus needed to think this through, or perhaps because they aren't interested in this problem)?

I know much more about free will and moral responsibility than about scientific realism so I can say which much more confidence that someone who thinks that 'free will vs. determinism' is a big question in philosophy doesn't understand what philosophy is up to. The relevant issues in philosophy are 'what kind of freedom is required to justify our practices of holding people responsible for what they do?' and 'can this kind of freedom exist in a deterministic world?' The question whether or not the world is deterministic arises only for the those who answer the latter question with 'no'.

Methodological naturalism is another one of my favorite subjects and I agree that the idea that science is restricted to methodological naturalism is dead wrong. This is, however, a minority view among both scientists and philosophers and presumably Larry knows that very well (I assume he has read most of the responses he got on his view that creationism is science). However, I fail to see why the fact that so many of my fellow philosophers do not agree with my position would show that they aren't good philosophers or that their position is not respectable.

John Wilkins says on Facebook that you have given the "correct" answer.

You said,

"I do not see that many philosophers throw unreasonable doubts on answers they should reasonably accept and that they do so either merely "because they like to quibble" or solely because the obvious answer doesn't fit their worldview."

Let's talk about methodological naturalism. You say that the idea is dead wrong and you also say, "This is, however, a minority view among both scientists and philosophers and presumably Larry knows that very well ."

I'm glad you agree with me that it's dead wrong but I DO NOT know that this is a minority view among philosophers. Ten years ago I had trouble finding a single philosopher who would speak out against Michael Ruse, John Haught, Robert Pennock and a host of other philosophers who say that science cannot investigate the supernatural.

It was Maarten Boudry and the Ghent group who opened the floodgates to widespread criticism of methodological naturalism. I was at the talk he gave in Toronto at a meeting of philosophers and it pretty much fell on deaf ears. Maarten was only a graduate student at the time. Even now, there are very few other philosophers who openly criticize methodological naturalism. (When's the last time you saw a philosopher telling Michael Ruse that he's dead wrong?)

The presumed limitation of science (methodological naturalism) is the keystone of AAAS and NCSE policy because it provides an excuse for saying that science and religion are compatible. Most of the philosophers who defend MN are religious and I claim that they do so because it fits their religious worldview. Even atheist philosophers who defend MN seem to do so because they don't like the alternative and they want to accommodate religion.

We are coming up on the tenth anniversary of Kitzmiller v. Dover and there's going to be a lot of hype over this "victory." The NCSE crowd are going to laud Judge Jones for proving that ID isn't science and that's based on testimony from MN proponents.

Here's what Jone said in his decision, "It is therefore readily apparent to the Court that ID fails to meet the essential ground rules that limit science to testable, natural explanations." Now, if it's true that limiting science to testable natural explanations is the minority view among philosophers then now is the time to speak up.

Not holding my breath. Are you going to write something? I'm pretty sure John Wilkins isn't because he's part of what you say is the "minority" view. John says that methodological naturalism "is the underpinning of all science, and indeed all learning about the world" [John Wilkins Revisits Methodological Naturalism]. Arno, have you told him that he's dead wrong?

This is an excellent example of where philosophers seem to be out of touch with reality. Scientists have been investigating, and refuting, supernatural claims for centuries without noticing that they're not supposed to do that.

So there really are scientists who don't strive for theories and models that describe an underlying reality and who don't think that striving for such theories is a hallmark of good science.

Some philosophers are interested in what traditional scientist (physics, chemistry, biology, geology etc) do in their day-to-day work. As a general rule, those philosophers don't spend a lot of time in laboratories studying their subjects. Instead, they prefer to theorize about what science is.

In turns out that probably 99.9% of what scientists do is attempt to understand the nature of the universe and they sincerely believe that what they are working on is real. Scientists build models and theories to help them make sense of the universes and those models and theories are supposed to represent real things and what's really going on.

Philosophers have discovered a few scientists among the 0.1% who don't care if their theories and models reflect reality. Most of those scientists are kooks (e.g. Intelligent Design Creationists) but some are legitimate scientists.

Because of this tiny minority, philosophers have constructed elaborate theories about the nature of science and whether naive realism, structural realism or anti-realism (or a host of other views) represent what scientists actually do when they investigate the workings of the universe.

This is an excellent example of a discipline that's way out of touch with reality. If you restrict "science" to the traditional disciplines (I don't) then the proper way to describe what scientists do is to say that science investigates the nature of the universe and it's equally proper to say that scientists investigate real things and real phenomena.

You can add a disclaimer saying that there may be minor exceptions to the rule, even among legitimate scientists, but it's a gross exaggeration to construct elaborate theories of science based on those minor exceptions.

From my perspective, saying that this is a '"hot topic" in the philosophy of science and defending diagrams like the one at the top of the page is a damning indictment of the philosophy of science. It's quibbling and nitpicking. Don't philosophers have anything better to do with their time?

Want a suggestion for something better to do? Try convincing the general public that there is no god. That would be much more useful and it's a genuine philosophical issue where, presumably, most philosophers can agree.

“The relevant issues in philosophy are 'what kind of freedom is required to justify our practices of holding people responsible for what they do?' and 'can this kind of freedom exist in a deterministic world?'”

I agree that this is the zeitgeist of a certain analytical approach to the free will question. I will grant that not many analytical philosophers take differing approaches seriously, but behavioral scientists, say, could shrug at the idea that moral responsibility is a concept that has anything to do with determinism or with free will (unless you define such as the ability to make free decisions carrying moral responsibility). Such behavioral scientists could see the desire to connect responsibility to free will to be as an unimportant and unenlightening task as exploring the game of schmess (irony aside). That is, scientist and contrarian philosophers could disavow that responsibility and free will have anything to do with each other, other than a happenstance discursive entanglement, one whose documenting simply makes one an historian or sociologists of some stripe. And not some one who is trying to arrive at a useful description of determinism (including humans). Also, in the end, I claim such philosophy is not going to give a good accounting of human social practices, given the messy entanglement that they are unwilling to disestablish between asking about the social world and the idea of determinism.

The willingness to stick within that discursive realm, say the social-practical-linguistic realm, is not the mark of people who want to first give us a good accounting of worldly phenomena in most instances. This is where philosophy's role of still hosting god arguments and still attaching religious studies to many of its departments gives many people great pause about whether philosophy truly wants to give a good accounting of determinism, realism, evolution, god, etc. These are areas that scientists are confident that religion and social discourses should not be given useful say in delineating our best explanations. Most scientists recognize that religious authority and social beliefs should not have a say in determining the reality of prayer or in the reality of souls, along with most other phenomena, both worldly and more human centered. Similarly, saying that a machine or brain/machine can make decisions by its own internal processing (without overt external manipulation) is not to say anything very useful about the world.

To rephrase Larry's point a bit, there may be questions to be asked about the reality and structure of scientific concepts and progress, but these disputes should not have us question a more basic realism or a more basic belief in accrual of knowledge. How exact our heliocentric models are to reality can be disputed. What cannot be disputed is that we gained some (realistic) understanding of the world when we accepted the general heliocentric concept. Those models, beliefs, and worldviews, which arose out of science (broadly construed), went beyond methodology in nature to a revised and better understanding of the world. Many scientists are not going to listen for a second to programs that cast doubt on the last assertions. And for good reason.

Note added when posting: I tried to post the following comment several times but apparently I did not succeed in getting it trough. It is a response to Larry Moran's reply of Thursday, September 17, 2015 8:13:00 AM. It was written before his reply of Thursday, September 17, 2015 8:41:00 AM appeared on my computer.

Thanks very much for your elaborate response, Larry!

I am afraid, my English was mistaken. I intended to say that the view that science is restricted to methodological naturalism is dead wrong is a minority view, not that methodological naturalism is a minority view. In Dutch (my native language) the demonstrative pronoun 'dit' (usually translated as 'this') at the beginning of a sentence refers to the object of the preceding part ("the idea that science is restricted to methodological naturalism"), but I should have realized that in English 'this' always refers to the preceding noun phrase ("methodological realism"). Sorry for the confusion.

I would be very interested in your evidence for the claim that "most of the philosophers who defend MN are religious" as well as in your arguments for the truth of your insinuation about their motives.

When I was a graduate student in the 1980s my dissertation supervisor and most of his students agreed about the wrongness of methodological naturalism, but it was clear to us that this was a minority view among both philosophers and scientists. I cannot remember how often scientists have scorned me for my refusal to a priori exclude appeal to gods from science, but I am sure that most who did were atheists. A few years ago an outspoken atheist evolutionary biologist immediately assumed that I was *defending* (rather than attacking) Intelligent Design when I said on his Dutch blog that I see no a priori reason to exclude gods from evolutionary explanations! I do remember having said to Michael Ruse that I did not accept methodological naturalism, but it didn't impress him of course and I do not think he remembers it (probably he does not even remember me).

However, as I said, I mentioned methodological naturalism, because I fail to see why "the fact that so many of my fellow philosophers do not agree with my position would show that they aren't good philosophers or that their position is not respectable."

In your view, on the other hand, methodological naturalism is "an excellent example of where philosophers seem to be out of touch with reality".

It is the business of philosophy to work out different views of the nature of science. If we are discussing views that are totally irrelevant outside philosophy that would be a good reason to dismiss those views as out of touch with reality. However, methodological naturalism is relevant to many issues outside philosophy (as you yourself indicate by referring to Judge Jones). I would be very interested to hear why the fact that Boudry, you and I disagree with that view would make it (=methodological naturalism) out of touch with reality.

Larry, I hope I haven't given the impression to claim that the reason philosophers have constructed elaborated theories of the nature of science lies in the existence of a tiny minority of scientists who are anti-realists. That would be absurd. I think did so because they are interested in the nature of science and discovered that their initial ideas about this nature had problems or couldn't stand scrutiny. At least that is how I became interested in most of the philosophical problems in which I am interested in (as I said, scientific realism is not my favorite topic).

I also like to emphasize that I did not mean to defend anti-realism. Rather, I wanted to suggest that your idea that the philosophical discussion of scientific realism is questionable might rest on a misunderstanding of what that discussion is about: it is not about the nature of reality as you suggested in the OP, but about the nature of science.

I also wanted to point out that the *feeling* that a certain position is bizarre is not a good reason to reject it: what is obvious to one group of enquirers might be bizarre to others. That's the reason why I pointed to the fact that "there really are scientists who don't strive for theories and models that describe an underlying reality and who don't think that striving for such theories is a hallmark of good science."

In response, you claim that it "turns out that probably 99.9% of what scientists do is attempt to understand the nature of the universe and they sincerely believe that what they are working on is real. Scientists build models and theories to help them make sense of the universes and those models and theories are supposed to represent real things and what's really going on" and "the proper way to describe what scientists do is to say that science investigates the nature of the universe and it's equally proper to say that scientists investigate real things and real phenomena."

The claim that 99.9% of the scientists "sincerely believe that what they are working on is real" is a psychological claim. If I were interested in that claim I would ask you for references to empirical studies of the beliefs of scientists in support of your view.

In the other parts of this quote you take a stance in the debate on scientific realism. If I wanted to discuss scientific realism with you I would now ask for arguments for your view and if you're answer would be that this is what 99.9% of the scientists believe they do, I would point out that claims about the number of people believing x don't provide evidence for the truth of x. On the other hand if you would reply that trying to develop models that represent real things is the best way to make sense of what scientists do, I might ask how you would refute arguments to the effect that models and theories need not represent reality in order to make sense of the world. Or whatever.

But I am, at the moment, not interested in discussing scientific realism, but in your claim that the discussion is moot. In fact, I have a question for you: isn't it a bit strange to claim on the one hand that the discussion of scientific realism is moot and on the other to insist on a certain position within that discussion? Isn't that a bit like an atheist who tells believers in what God they should believe?

You write: "From my perspective, saying that this is a '"hot topic" in the philosophy of science and defending diagrams like the one at the top of the page is a damning indictment of the philosophy of science. It's quibbling and nitpicking. Don't philosophers have anything better to do with their time?"

I am moved by your concern for my discipline, but, frankly, isn't it a bit presumptuous to take the fact that we are interested in topics you aren't interested in (or, perhaps pretend not to be interested in) or that we are interested in positions you don't like, as a sign that there is something wrong with us?

No one seems to have pointed out the core problem with this "debate": there are at least as many potential interpretations of what "real" means in this context (and hence of what the topic of the debate _is_ in the first place) as there are participants in the debate. Larry mentioned electrons and selection coefficients as examples, but we have no idea which of the participants have in mind an interpretation under which both of these are "real", vs one but not the other, vs neither. Surely the answer depends almost entirely on what we mean by "real" (which could be virtually anything, and almost certainly is interpreted in vastly different ways by different people, even those who are in complete agreement on everything else in the debate) rather than on the nature of electrons and selection coefficients (on which we are much closer to consensus). Before having a debate, shouldn't there be at least some attempt at trying to establish common ground regarding the topic of debate and the meaning of the words used in it?

Hi Lyndon, I am very sorry, but I don't understand what you are saying. You use too many words and phrases that are unfamiliar to me, too many complicated sentences and you refer to too many ideas and issues I don't know about. If you are trying to explain what Larry is saying, spare yourself the trouble. His English is much clearer to me than yours.

Lyndon Page writes: "there may be questions to be asked about the reality and structure of scientific concepts and progress, but these disputes should not have us question a more basic realism or a more basic belief in accrual of knowledge."

It occurred to me that perhaps here again surfaces a misunderstanding about the topic of the debate on scientific realism. As I said above that debate is not about the nature of reality, but about the nature of science. Anti-realism, as far as I know (it is not my favorite subject and, hence, I have probably not stayed on top), does not dispute the reality of the world studied by the sciences. Far from disputing a basic belief in the accumulation of knowledge, the main motivation of anti-realism in het philosophy of science has been to understand how knowledge can accumulate despite the fact that the subsequent theories of the same domain (e.g. Medieval Aristotelianism → Newton → Einstein) posit entirely different ontologies. Now, the phenomenon that subsequent theories of the same domain posit entirely different ontologies is more common in physics than in biology or chemistry, which might explain why biologists are not interested in this problem. However, why would the fact that a certain problem does not occur in biology be a good reason to reject that problem as non-existing or to confabulate questionable motivations as an explanation for why philosophers are interested in that problem?

Hello Arno. I'm neither a philosopher nor a scientist, so forgive the lack of sophistication of my reply.

It seems to me that at least Newton and Einstein did not posit entirely different ontologies.

With regard to medieval Aristotelianism and Newton, perhaps it is the case that the difference in ontologies is what permitted the accumulation of knowledge. Or to look at it in the reverse way, to the extent that medieval Aristotelianism would have continued to hold sway, why would we have expected knowledge to accumulate?

QUOTE: "For example, many philosophers are theologians and they still argue for the existence of gods"

Let's use more informative quantifiers: i.e. *most* philosophers are atheists, some surveys put the number above 70%. A quick search on Duckduckgo or Google Scholar will get you a few papers on the topic. Also, most phil blogs have picked it up, along with sites like io9: http://io9.com/what-percentage-of-philosophers-believe-in-god-485784336

Science doesn't exist. Its just people, tailless primates for some, thinking about things to figure out things.The people still know nothing, heal nothing, and well nothing.Any conclusion by people is very likely to be corrected by other people in a little while. So on.Evolution is case in point. it has not been proven to be true yet claims to be a scientific theory. I have never seen any evidence for its truth or even a good chance to be true.

Dismissing God/Christ as proven to be not true is premature in most peoples minds.Human accomplishment is still very little relative to natures glory.Humans make great conclusions while not understanding almost anything in its workings. The lack of healing is proof of this.

What an incredibly ignorant, arrogant, and demonstrably false thing to say.

"The people still know nothing, heal nothing, and well nothing"

People know and heal nothing? ("well nothing" is gibberish; not sure what you were trying to say there).

Then explain this: On average, every two minutes a child dies of malaria. 24/7/365.25. That is reality, Robert. And your omnipotent, perfectly good god does nothing. If (s)he/it cannot fix this, (s)he/it is not omnipotent. If (s)he/it can do something about this, (s)he/it is evil, or else completely indifferent to human suffering.

Also, just 25 years ago, it was a child every one (1) minute dying of malaria, 24/7/365.25. Reducing the death toll of children to malaria was not achieved through prayer, or people giving their money to their church, or some "revelation" from the bible. It was done by people (yes, we 'tailless' primates, and we all are, Robert, except for that time in utero when we start to grow tails like our ancient ancestors but resorb them during development, another clear evidence of common descent and refutation of 'intelligent design') doing science, developing methods to control the vectors of malaria, and exposure to them; discovering medicines to combat malarial parasites, etc., etc., and sheer force of will to implement these scientific advances to save lives. While your god did zero (0).

I'd like to postulate, this designer/ god what ever, actually hates the life he/ she/ it created. It's trying everything in it's power to kill all life using bacteria, viruses, other life killing other life, rocks from outer space smashing into the planet, bits of the planet too hot or too cold to live in, a sub optimal ozone layer allowing UV radiation to bake the skins of people into melanoma's. Bacteria get wasted by phages. Parasites crawling in paralyzed animals, using the not dead host as food.

Clearly life wasn't what the designer wanted, but for some reason it popped up and he/ she / it can't seem to get rid of it...

Chris B Actually it was God that led a few people to figure out how to deal with a few diseases.Your claim that a few things is done does not discredit my opinion very little has been done. One must be aware of the health problems that kill and hurt and don't allow longer life. I insist very little healing has been accomplished. Its relative but it shows it takes people to do it. Its NOT science as a tool.

Science doesn't exist. its just a method to help establish conclusions. Even then its not well done as evolutionary theory claims proves.Its just people thinking about things. Sure it is.People never had tails by the way. Its an error again of research and reasoning.

Byers demonstrates his supreme arrogance with : Science doesn't exist. its just a method to help establish conclusions. Nope - it is a method for learning about the REAL world (and the collection of gained data). Such as what is in the world, how things ACTUALLY work, how things came to be the way they are, etc.Even then its not well done as evolutionary theory claims proves.

Actually, it is done exceedingly well (given how much we've learned about the world in just a few centuries). Were science done like creationism, we'd still be living in caves, poking each other with sharp sticks and sacrificing people who disagree with us to the Magical Sky Pixie that makes it rain.Its just people thinking about things. Sure it is.

AND THEN GETTING OFF THEIR RUMPS AND TESTING THEIR IDEAS ABOUT HOW THE REAL WORLD WORKS AGAINST THE REAL WORLD. This makes science vastly superior to the arrogant, self-absorbed navel gazing of creationism. Having the ABILITY to test claims makes science better than creationism; actually having the GUTS to do so leaves your cowardly gibberings light years behind.People never had tails by the way. Its an error again of research and reasoning.

Nope - IT IS AN OBSERVATION. During fetal development, humans do have a tail - an extension of tissue that extends beyond the body. Sometimes, even today, people are born with vestigial tails. Medical practitioners even have to distinguish between true vestigial tails and pseudotails - a true vestigial tail is relatively benign; a pseudotail is tissues and fluids inside a pouch at the base of the spine, and can mean problems.

Examination of human DNA shows we still have genes for egg yolk proteins - they are badly degraded, but still present.

"Actually it was God that led a few people to figure out how to deal with a few diseases."

What is you evidence for that? Why did he create diseases to inflict his other creation with?

"Your claim that a few things is done does not discredit my opinion very little has been done. One must be aware of the health problems that kill and hurt and don't allow longer life. I insist very little healing has been accomplished."

Apparently you weren't paying attention to my post. The sheer magnitude of the misery and death that malaria inflicts on the human species is enormous, and to claim that about halving the childhood death toll from it constitutes "very little has been done" is irrational and wrong. Your opinion was totally discredited with that one example.

"Its relative but it shows it takes people to do it. Its NOT science as a tool."

Of course it takes people to do it. It is a human activity.

"Science doesn't exist. its just a method to help establish conclusions. Even then its not well done as evolutionary theory claims proves.Its just people thinking about things. Sure it is."

The fact that a sentient human can sit at their computer, hooked up to the internet, in their nicely constructed home, not dead from smallpox or a variety of other diseases, not dead from tooth abscesses, etc., and write those sentences, and think they are making a logical statement is astounding. You proved yourself wrong! You owe me a new irony meter, this one just exploded.

"People never had tails by the way. Its an error again of research and reasoning."

No. The tail thing is a wrong interpretation of fetus development. Healing a great dsease still is only one thing. Even then its a special case of how they reverse it to kill the disease. I wish there was great healing results but its chump change relative to the problems. They have done almost nothing.Its about people with insights and its not about a tool called science.Science is a minor method to sure up conclusions better then regular investigation.Its not the spark of discovery or invention.There is no such thing as science as its used as a noun. Thats why error, like in evolutionism, is the result of people and not SCIENCE.Very little intellectual accomplishment has been done by mankind relative to our numbers and what can be accomplished.In fact its possible telling people conclusions come from SCIENCE as opposed to people is what slows done innovation and correction.

Paul Poland.The things you call tails are not evidence of tails but only need be seen as extensions of a fetus growth. not evidence of a past tailly heritage. Thats just a line of reasoning. People don't have tails and never did. Its a myth.

Wrong again, Robert. Why do creationists think that their delusional musings about the natural world somehow refute actual empirical evidence? Science is not a game of 'Yes it is! No it isn't!'. That is the realm of religious thinking. You can't import that here.

"Healing a great dsease still is only one thing."

But it is something. That's better compared to prayer, biblical revelation, and the acts of your imaginary god, which have done nothing.

"Even then its a special case of how they reverse it to kill the disease. I wish there was great healing results but its chump change relative to the problems. They have done almost nothing."

Again, i have to point out, almost nothing would be better that just nothing, which is what you bring to the table.

"Its about people with insights and its not about a tool called science.Science is a minor method to sure up conclusions better then regular investigation.Its not the spark of discovery or invention.There is no such thing as science as its used as a noun.Thats why error, like in evolutionism, is the result of people and not SCIENCE."

Stop saying such utter nonsense about science, Robert. We have been over this ground before and you have yet to refute anything anyone has said here, or in any other thread on this blog. You just repeat the same inanities over and over again. I can't even comment on the rest of your post. It is so divorced from reality that refuting it would be redundant and futile; like staring at an eclipse of the sun. But anyone who can talk themselves into believing in YEC is so irrational and delusional that there can be no reasoning with them.

Thanks for reminding me why I should never try to engage in a discussion with you.

The tail thing is off thread but i'll show why its not evidence for people once having tails.when people grow as fetus anything can go wrong. two heads or 12 toes or eight fingers and many other things. My mother as a nurse saw everything can be distorted in the human body.NOW the spine etc is a major matter in our bodies. It grows to a length needed. So in the equation of error its easily predicted that it would overshoot for some. in fact if we never had tails it would also be this way that some babies would have these extensions/tails.its not evidence of tails but only a probability matter of dysfunction in growth relative to percentages.We never had tails and those born are simply having over extension of the spine etc etc. That is accurate scientific investigation by thge way. not making the first conclusion on superficial data.

"when people grow as fetus anything can go wrong. two heads or 12 toes or eight fingers and many other things. My mother as a nurse saw everything can be distorted in the human body."

Why does your benevolent, omnipotent, all-loving god allow these horrors to happen to his creation? Is (s)he/it really that sadistic? Never, mind, theologists haven't come up with a whisper of an answer to that for centuries.

Anyway, the formatiom of the tail happens in EVERY human fetus. It is not an anomaly, it is a leftover from our ancient primate ancestors who had tails.It is a normal part of our fetal development. Full production of a tail has been suppressed by changes in the expression of developmental genes, another powerful line of evidence for common descent and evolution.

You are wrong, and no rational interpretation of data gets you to creationism, much less to YES. That is completely delusional. Feel free to live your life that way, it's yours to live. But don't some on a science blog and expect people to believe your fantasies in the complete absence of any credible evidence.

YES? They drove progressive rock awat decades ago. Actually all rock went with it.Anyways.The fettus does not need to be seen as having a tail. Its just a extension of the spine, I think, and a part of growth in the fetus. your saying this option is not allowed for some reason. If it was just a normal part of fetus growth then, in a probability equation THERE ALSO would be some babies born with the extension. Yert its not a actual tail or a tail at all.The clue is, you introduced me, that its nomal in all fetus. Not a relict but fully part of growth.Its a line of reasoning. Too quick to see the fetus extension probability number as evidence of a tailly past.how do you know its not fully normal for a fetus to have these extensions when doing the important thing or organizing the spine.?

I see your knowledge of music rivals that of your command of science. It's almost comical how you make demands of evidence of science completely at odds with reality, yet your armchair musings are gospel truth in the complete absence of evidence. Almost comical, because it is at the same time so sad.

YES was part of progressive ROCK that was targeted by the PUNK movement and others . I like some YES songs but they were making ROCK into JAZZY sessions. There are good youtube historys on Progressive ROCK and its enemies. I know this stuff and origin stuff.I think my probability example for fetus is the actual origin for "tails". Not a relict from when we had tails. Why am I wrong??

Robert, I'll agree Yes was prog rock and targeted, often rightfully so, for their excesses and choices. Often the criticism was unfair as well. Music is a subjective thing. But overall, they produced a good body of work and some truly remarkable, timeless gems. They flirted with jazzy but in my opinion didn't hit that full on until the Drama album, with mixed results and not much memorable music despite the excellent musicianship. But i digress :)

WRT the mammalian tail, you are correct in that the tail is of course an extension of the spine. Throughout mammalian evolution, the tail has had many different lengths, controlled developmentally. Several groups of mammals have evolved shortened tails, including bears, lagomorphs, many bats, some rodents (where their remarkable evolutionary diversity has resulted in lots of morphological range). We are no different, nor are our closest relatives, the other extant apes. The "fetus extension probability" is in fact a potential developmental evolutionary pathway. Tails may get longer or shorter. When you see the fetal development of tails in EVERY extant mammal, this is evidence for common descent. Even allowing that the tail extensions may be important for 'organizing the spine', this is fully compatible with evolutionary theory. Let's say it is absolutely necessary for organizing of the spine. Perhaps that is why we still develop a short tail which is later resorbed once the spine has developed. This still shows common descent with all other mammals.

What would be the ID/creationist explanation for our transient fetal tail?

Our fetal tail, explanation, is as I said. Just part of the organization while in the fetus stage. not a tail but a extension of the spine. We uniquely walk upright and so our spine is needing more flexibilty or something like that.The few cases of babies born with tails need only be seen as probability results from the common extension in all human fetus. Its not a special case of a relict tail appearing but just a wee bit more that didn't absorb in the spine. In fact one could predict this result without any reference to having had tails once in our past. I;m making a roll of the dice equation of error of the developing fetus which simply didn't absorb its spine extension.

In fact one could say whether we all were born with tails or none it would be irrelevant to our heritage of whether we had once tails. All one needs to know is the fetus has a "tail" whle growing. If thats proof of a tail past then thats the proof. if its not proof then having some babies born with the tail is easily explained away as a probability result of error of the fetus tail.The big clue is the fetus tail. If the fetus did not all have a tail you would have a better case.

Vertebrates including ourselves have a tail during fetal development. That's normal, not an error. The great majority of us humans resorb it, but a few are born with a tail.

No one fact proves evolution or the fact that we once had tails, but our fetal tails (and the tails occasional humans are born with) fits very well in evolution theory. One more bit of data fitting together. Our fetal tails don't fit well in young-earth creationism. Our fetal tails don't by themselves disprove the YEC position, but they are one more fact (among the thousands of facts) that don't fit.

They don't hurt creationism if they don't make a evolution fact.YEC easily can sae the extensions of the spine in the womb as a natural part of spine growth without any hint of being the relict of having rails formerly. THEN the rare cases of babes birn with tails is only a probability factor of error likely to happen where the extension was not absorbed.Its one thing and not two. Seeing tailed babes is missing the point of all fetus being tailed. In fact it makes no case AT ALL if the evidence for tails is the fetus tail. If the fetus tail is not evidence then neither is the tailed babies.A line of reasoning on top of data.

1. Biology is not messy, its barely understood. Evolution aids in the misunderstanding of biology, making is messier not better understood. The best evidence for this is the number of patches required to link the variety of evolutionary concepts out there. The more the patches, the weaker the explanation. Like Windows 10, its not a pretty picture.

So lets just drop the pretense and dispense with the concept of evolution altogether.

2. Species is hard to define precisely because it is being misused to describe what we observe as variety. There are no species of birds, only varieties of birds. See now, variety of birds is much clearer and easier to define than species. Therefore, variety if the more appropriate term for the kinds of birds we observe. Problem solved.

A good point here. There is more difference between types of people population groups then between recognized species in the animal kingdom. The species of bears is less variable then people groups.so why not call these people groups species if species is a reel thing in nature??they can't say its about reproduction. They mate lions and tigers. What is the origin of species is probably the problem of defining what/if a species is.

When dealing with sexually reproducing organisms, the species definition is about reproduction. The basic definition we learn in high school is something like, "A species is often defined as a group of individuals that actually or potentially interbreed in nature and produce fertile offspring." In other words, the individuals are members of the same gene pool. Clearly, humans of all races can breed together and produce fertile offspring, so we're all one species.

Lions and tigers don't normally interbreed in the wild, and when humans cage them together so that they do so, the male offspring are sterile. They aren't the same species.

There are several real-life complexities that make our preferred species definition hard to apply. What if the individuals live in two separate places (e.g. mainland and island) and never normally meet? The island individuals are similar but also somewhat different; should we call them different species or not? What if the individuals live together and do meet and usually don't interbreed but rarely do, and the offspring are fertile? What if there are two consistently different groups of individuals and they mostly breed only with their own kind, but in one geographic area or in a disturbed intermediate habitat, they do interbreed readily and produce fertile offspring? What if the individuals only reproduce asexually (clonally)? What if they usually reproduce asexually but do interbreed occasionally? (These can be the worst for classifying.) What if there are lots of individuals that look the same to us but turn out to have subtle chemical differences and can tell each other apart and treat each other as five different reproductively isolated groups?

We humans need to give names to the groups of similar individuals so we can talk about them and store and retrieve information about them. We call these units "species." We can't apply our preferred, basic definition to all of these cases. I personally (as a plant taxonomist) use our preferred basic definition when I can, and if I can't I run down a list of different definitions until I find one that applies to the example I'm working with.

bwilson295Yet they do breed lions and tigers and whales and dolphines and so on. Even if one is sterile it still reproduced.Saying a species is only about ongoing reproduction would mean species is only about reproduction. Not actual biological segregation.People groups are more different then lions/tigers or dolphins/whales or anyways heaps of species not proclaimed. YEt people are not said to be differenbt species.OKAY. then its not looks but ONLY reproducing.m successfully. CASE CLOSED.If its just that then thats that. BECAUSE many species look more alike then people groups look alike.So the origin of species is the origin of population reproduction perfection.one could say selection on traits is not the origin of species unless it produces reproduction boundaries.This is not what they teach today. It would mean minor traits in a population could lead to reproductive exclusion while great diversity in traits not lead to it.like in domesticated dog breeds which never leads to reproduction interference but, I think, canin species are exclusive in the wild.

Humans are diverse and we can all breed together to produce fertile offspring. Therefore, we are one species.

In some groups of animals, individuals in one species may resemble all the individuals in another species much more than some humans resemble other humans, and yet we could these animals as two different species because they do not interbreed. Very true.

Yes, ideally, the origin of a new species is completed when reproductive isolation between two groups is perfected.

Yes, one could say that the origin of new species depends on traits that produce reproductive boundaries, not on selection for other traits. It is important to remember that selection for one trait that is not about reproduction may lead to reproductive boundaries. For example, if selection causes animals in one place to be tall and animals in another place to be short, eventually they will not be able to interbreed. Also, sometimes the genetic changes that cause reproductive boundaries were not selected for, but are accidents.

You wrote, "It would mean minor traits in a population could lead to reproductive exclusion while great diversity in traits not lead to it.like in domesticated dog breeds which never leads to reproduction interference . . . ." This is true. (However, if most dogs died leaving only a few kinds, like big Great Danes and tiny Chihuahuas, they would be different species because they could not interbreed. Dogs are all one species only because of all the intermediate forms between the extremes.)

You wrote, "but, I think, canin[e] species are exclusive in the wild." That is pretty much true, although there are hybrids between coyotes and dogs and hybrids between wolves and dogs, and hybrids between wolves and coyotes.

You wrote, "This is not what they teach today." The true things that you have written here are taught today in many schools, and should be taught in all of them.

Bwilson 295Then you seem to be saying that without perfect reproductive exclusivity there is no species.So the origin of species is only from what made the reproductive isolation for a population.SO however great the diversity in traits is between groups that are alike it still doesn't qualify as speciation.I understand all domesticated dogs can breed without sterile issues. so i don't think your intermediate comment joining the extremes of dog types in size is true. They are all one species despite looks. Yet if found in nature they would be classed as different species UNTILL it was found they could all breed together using your rules.

Yet it seems to me, like bears, theu class them in species without regard to reproduction ability. I know they struggle over Canada moose and Eurasion moose. Some call them different species and others races. I think they all can breed fine together.Therefore if people evolved their different looks.then its only chance they didn't go a bit further in changing and so not be able to breed together.People are more different then many creatures divided by species despite likeness.

Anyways if reproduction is the origin of species then its not Darwins idea of selection on traits. He would see first the selection on traits and only later a reproductive isolation issue. SO it would mean there is a intermediate stage. SO people could be said to be in that stage and only our present mingling stopped a reproductive isolation between people groups.There is so many ways one can look at this.

As a yEC I don't think species exist. Rather there is just change in a original population from different influences with results in different looks etc. If its so much a difference that they can no longer breed together/or without sterility issues then its just a coincedence of how much the change affected the dna.I think the changes come from innate triggers and hardly much minor selectionism on traits.Thats why the origin of species is a problem. there are no species and no rules therefor.

Robert, you're not really right here. There is nothing about the importance of reproductive boundaries in the origin of species that contradicts the idea of natural selection. Sometimes natural selection acts directly on traits that affect reproductive boundaries. Sometimes natural selection acts on traits the indirectly affect the ability to interbreed. (For example, if selection for small size affects one population and selection for large size effects another population, eventually the two populations will be so different in size that they cannot interbreed.) Sometimes natural selection acts on some traits and eventually, just by accident, some other mutations cause reproductive isolation. (In this last case, the reproductive boundaries may result from neutral evolution, not from selection.)

You are right that Darwin's ideas about species means that there is an intermediate state between being one species and being two. First there's one species. Then it divides into two groups. The the groups become more and more different. Eventually they become two species. When we look very carefully at the different kinds of organisms, we do see some populations in an intermediate state, between one species and two. (I see this in my plant work, as Darwin saw in his barnacles and his friend Hooker saw in his New Zealand plants.) We also see lots of plants and animals that are clearly distinct species.

Its an involved subject.my only angle was that if a species IS ONLY a species IF unable to reproduce/without sterility that what a species IS would be settled in biology.It seems to me they created species and still define species unrelated to whether there is a reproductive barrier.I know moose is a issue on this and I suspect bears can interbreed fine and deer or the like. Yet called different species.You say there is a intermediate stage as there must be if evolution was accurate. so the intermediate would not be a species.would your plants all be ruled by this law? I'm unsure about the scoring .A threshold must be crossed at some point to justify the origin of a new species. Up to that point its still the same species.I suspect Darwin never had the reproductive barrier or even knew if there was one in the creatures he thought about or talked about.He said natural selection was the origin of species regardless if reproduction isolationism had taken place.I don't think his finches or anything he presumed they couldn't interbreed or even thought about or presumed they couldn't.It would mean the reproductive threshold is very important and I don't see it brought up when there is teaching about how species evolved. almost after the fact. The big facts are the big looks changes.something here for creationists to press home i think.

We find different conditions. Sometimes, two sister species (species with a relatively recent common ancestor) live together and don't interbreed at all. Those are the easy cases. Sometimes we think about calling two somewhat different forms two different species but we learn they interbreed a lot, so we decide they aren't two different species (yet). Those cases aren't too hard.

Much more difficult are cases where we have two different forms -- different colored birds, or flowers with somewhat different structures -- and they usually don't interbreed but sometimes they do, or the offspring are mostly fertile. Those are harder cases, in between being one species and two.

Darwin and the other botanists and zoologists of his day didn't know much, if anything, about population genetics. However, the spent a lot of time studying patterns of variation. They understood that sometimes groups of populations (different species) differed consistently in their traits. (This was because they didn't interbreed.) They also understood that intermediates are common or rare between other groups of populations (species) and that this was a problem for the simple taxonomy system. Biologists of the time thought that species were created and did not change, but if that was the case, there shouldn't be intermediates. However, every large group studied have obviously different species and obvious variation within species, and also variation that was sort of like two different species and sort of like variation within one species. This was really important evidence of change. Darwin studied this a lot. One reason many biologists of his day so quickly accepted evolution theory was that it explained the intermediate states, the cases where maybe there was one species but maybe there were two. No other idea before that had provided an explanation.

Thanks for your knowledge on this.i think there is still no final conclusions on what a species is.You mention some types of plants live together and never breed but its the issue CAN they NOT breed.Anyways for BOTH creationists and evolutionists I think the answer must be that from some parent population there was biological change in that population, whatever the mechanism, that led to a little or a lot of biological change. LOOKS different from the parents.The issue of whether they can reproduce completly or partially/sterilty issue is not relevant to the real biological system in the world. species is only a human construct and not a real one. its a myth. biology does not recognize species. Only variation from a parent population.for both sides i am confident this is the accurate answer and so thats why the species label doesn't work in too many cases.Interesting conversation on a matter i have noted conflicting views amongst teachers on biology.

No, it should not be written like that because there could be functional DNA that doesn't depend on a specific sequence. There are clear examples of such spacer DNA and there's a whole set of bulk DNA hypotheses that purport to explain most of the excess DNA in large genomes.

And, as you have mentioned on occasion, there are bits of junk DNA for which changes in sequence could give rise to either new functional sequences or to sequences with deleterious effects. Most of the average intron is junk, but if mutations cause a new splice signal to happen in the middle of the intron, there will be trouble. And so on.

I can see calling spacer DNA functional, but how is it possible to assume non-coding sequences of base pairs do not act as spacers? DNA coils in the cell are extremely complex, which is why I expect the relative positions of promoters and the genes they promote are likely to be affected in unexpected ways.Changes in the amino acid sequence for proteins far away from the active site can have remarkable effects such as allosteric regulation. How can this be ruled out for chromosomes? I was so surprised to read Watson's Molecular Biology of the Gene when it came out. If I remember correctly "chromosome" wasn't even in the index. But that was then. Hasn't our model improved since?

If bits of DNA functioned as spacers, we would expect their lengths (though not their sequences) to be conserved over evolutionary time. For most sequences (including, for example, introns) we don't see that as far as I can tell. Introns get indels at what looks to me to be a neutral rate.

Then I suppose you can then distinguish spacer DNA from junk DNA by the conservation of sequence length of non-coding base pairs. Introns incorporating indels at a neutral rate seems like good reason for calling them junk. Assuming tight control of spacers by natural selection implies we should assume non-coding DNA can be deleted without causing effects, i.e., most of it is junk.

Personally I would prefer not to call spacer DNA functional because it seems unreasonable to assume non-coding DNA has no spacer functions without positive evidence to the contrary. But I was never convinced that selection pressures on individual genes were so immediate, as opposed to indirect effects from natural selection of phenotypes.

In some cases there should be a minimum spacer distance but the maximum can be quite large. For example, you probably need at least 50 bp of intron in order to form the RNA loop in the spliceosome. Thus, I have argued that about 50 bp of every intron sequence has a function because it can't be deleted without causing problems for the organism. Most of the intron is junk - this takes up about 20-25% of the human genome. (About 25% of the human genome is devoted to protein-coding genes.)

Similarly, there's probably a minimum distance between some regulatory sites because you need to form a loop of DNA. This is known to be true for the two lac operator sites. The spacer is necessary. I think this qualifies as functional DNA even though the sequence is irrelevant.

Well, as occurs frequently enough when philosophy is the subject, I’m not sure I understand the totality of the argument about realness. However, if we provisionally accept that “things” in general are real, it seems strange to focus on whether genes are real (and if we cannot provisionally accept that things in general are real, than it is doubly nonsensical to focus on whether genes are real).

I suspect that in a least a few cases the question “are genes real” probably stems from a layperson’s understanding of the concept of genes as in: “genes are the blueprint for living things”, or some such thing. This is hardly correct and if coupled with the sense that there is no completely satisfactory single definition of gene, the layperson might indeed think the concept of gene to be a fuzzy, perhaps artificial construct.But if that same person understood molecular biology, they would know that genes are real. When expressed, you can correlate that with an increase in abundance of the matching RNA. When translated into protein, the protein increases in abundance and you could sequence the protein and show that the amino acid sequence is as predicted by the DNA sequence, etc.

Is it possible that, just as I shouldn’t opine too much about philosophy, some people shouldn’t opine too much about genes?

There is an old joke about a letter from the dean to the biology department: Your department is too expensive to run. Why can't you be like the math department? All they ask for are pencils, paper and waste paper baskets. Or more like the philosophy department - all they ask for is pencils and paper.

Robert said No. The tail thing is a wrong interpretation of fetus development.

Why? How come you know better than people who actually have studied such matters?

Why don't you question the fact that we have genes for the development of tails? Or six toes/fingers? You should rather ask "Why don't we all grow tails?"

How come the speculation you do in your spare time with nothing better to do, yield better and correct answers to questions than the answers arrived at by professional people?

You understand biology better than professionals, period.

That is proof you are an outstanding character, among the smartest people in the world! Don't you think you'd deserve at least a nomination to the Nobel Prize?

Since you are so super smart, I presume you'd understand cars better than automotive professionals if you only would discuss that subject. Why don't you apply your superior intellect to the subject of electric cars?

The world need to replace billions of polluting, fossil fueled cars with electric cars, and there are many problems that cry for a superior intellect to solve them as fast as possible. You'd become stinking rich as a side effect. Oh wait. You'd need science to do that.

This is an opinion piece, so i can as well contribute my opinion that philosophy is not only a colossal waste of time - see the diagram - but it is also a bad social influence - see the diagram again. If philosophy has no own means of judging meaningful questions and answers, it can be used to push religion and what not. And so it is.

It is very clear from the diagram that whatever the philosophical question of "reality" is, it is a bad question. Science has an entirely different question and answer, it studies nature and by its ability to study it we know of its existence. We also now know that it is all there is, the perhaps best way being the recent ability of cosmology to study nature (the universe) as an isolated system. (But we also know this from many other sciences, from thermodynamics over the vacuum properties of quantum field theory.)

This way of putting up nonsensical questions - "reality", "free will", "supernatural", "materialism", "scientism" - and never arrive to an answer is symptomatic for pseudo-studies. The sooner humanity drops the training wheels of classical greek society, the better.

Oh, I forgot: Larry mentions how philosophy is used to teach critical thinking in US. But if we apply it to philosophy, the subject falls to pieces.

I can't remember that there is a very concentrated effort in Sweden, we don't have the debate club idea for worse or for good. Critical thinking is area dependent (there are studies on children showing that they acquire some aspects early on, such as understanding correlations), and I assume we sop some up as we go. But we do make lousy debaters. =D

Laurence A. Moran

Larry Moran is a Professor in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

Sandwalk

The Sandwalk is the path behind the home of Charles Darwin where he used to walk every day, thinking about science. You can see the path in the woods in the upper left-hand corner of this image.

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Some readers of this blog may be under the impression that my personal opinions represent the official position of Canada, the Province of Ontario, the City of Toronto, the University of Toronto, the Faculty of Medicine, or the Department of Biochemistry. All of these institutions, plus every single one of my colleagues, students, friends, and relatives, want you to know that I do not speak for them. You should also know that they don't speak for me.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.